The Medical Schools Outcomes Database (MSOD) is an ongoing longitudinal tracking project of medical students from all medical schools in Australia and New Zealand. It was established in 2005 to track the career trajectories of medical students and will directly help develop models of workforce flow, particularly with respect to rural and remote shortages. This paper briefly outlines the MSOD project and reports on key methodological factors in tracking medical students. Finally, the potential impact of the MSOD on understanding changes in rural practice intentions is illustrated using data from the 2005 pilot cohort (n = 112). Rural placements were associated with a shift towards rural practice intentions, while those who intended to practice rurally at both the start and end of medical school tended to be older and interested in a generalist career. Continuing work will track these and future students as they progress through the workforce, as well as exploring issues such as the career trajectories of international fee-paying students, workforce succession planning, and the evaluation of medical education initiatives.